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Crystal structure of C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with 5-(aminomethyl)pyridin-2-amine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZCS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291.15 PEG 4000 19%, TRIS pH8 0.1M 6-7-8-9-10% guanidine HCL 5-6-7% Glycerol
Crystal Properties Matthews coefficient Solvent content 2.5 50.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.395 α = 90 b = 69.42 β = 90 c = 118.819 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2022-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.965459 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.95 59.94 99 0.099 0.113 0.052 0.992 7.6 4.3 27573 42.28
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 1.99 0.608 3.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.96 59.94 1.33 27573 1425 95.25 0.2441 0.2423 0.2422 0.2746 0.2746 55.64
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.1437 f_angle_d 0.7698 f_chiral_restr 0.0552 f_bond_d 0.0065 f_plane_restr 0.0056
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1041 Nucleic Acid Atoms Solvent Atoms 37 Heterogen Atoms 9
Software Software Software Name Purpose PHENIX refinement